In an interview with television station EMTV he said he had made his position known to the Speaker Theo Zurenuoc (pictured), who has been organising the destruction.
Mr O’Neill said the people have the right to be consulted before such measures are taken.
Parliament House was first opened in 1984, built in the style of a Maprik haus tambaran. The architecture is based on spirit houses found near Wewak in the East Sepik Province.
Mr Zurenuoc has a strong conviction that the spirits of the cultural relics are the cause of the evil and corruption that plagues PNG society and he has been ridding parliament of the ancestral relics.
Mr Peter O’Neill does not agree with what the Speaker has done.
He says the artefacts reflect a time in the history of PNG.
He said he understands the argument being put forward by Christians, but considers there is “a new way of believing”.